The Vatican Museums offer early-access tours that get you into the museums and Sistine Chapel before the regular opening hours. The Museums and Chapel tend to be really unpleasantly mobbed during the regular entry period.
Some Vatican-offered tours have in-person guides; for others you'd be on your own, but there's an audioguide available at extra cost. Private companies like Walks of Italy also offer early-access tours that are more expensive than the Vatican's. Online Vatican regular-entry tickets (especially) and tours sell out far in advance for much of the year. Even in the depths of winter, online tickets will not be available if you wait too late. Check your dates here:
Vatican Museum website
In the past, tickets for tours have been put on sale earlier than the plain-vanilla entry tickets.
One and a half days in Rome is a painfully short. I'd think long and hard about whether I wanted to spend a significant chunk of that limited time in the crowded Vatican Museums unless I could get tickets for an early-access tour. There's no substitute for St. Peter's (separate location with no entry charge) and the Vatican Museums from the religious standpoint, but if your primary interest would be the art, the Borghese Gallery is an option worth considering. These tickets also sell out in advance, but conditions in the Gallery are much more pleasant than in the overcrowded Batican Museums. The Borghese Gallery is a 2-hour visit.
Rome is full of beautiful churches, most of them free and without the very long security line you'll have to wait in at St. Peter's if you aren't able to use the door connecting the basilica to the Sistine Chapel.
You haven't told us your sightseeing interests: Ancient Rome? Religious Rome? Art? The atmosphere/markets/etc.? Food?